Protein 1619 of Pseudomonas putida WBC-3 participates in para-nitrophenol degradation by converting p-benzoquinone to hydroquinone

It is necessary to develop appropriate approaches to eliminate para-nitrophenol (PNP) in our environment, because the pollutant is highly toxic and also able to persist in the environment. Previously, Pseudomonas sp. strain WBC-3 isolated from polluted soil was found to be able to use PNP as the sole carbon and nitrogen source, but not very efficiently. In this study, WBC-3 was shown to belong to Pseudomonas putida through de novo genome sequencing. To enhance its efficiency of PNP utilization, a mutant strain (PM1-33) with a significantly increased PNP degradation rate was obtained. Although no increase in the expression levels of known PNP catabolizing genes/proteins were observed between WBC-3 and PM1-33, the expression level of protein 1619 significantly increased in PM1-33. Deleting GM1619 in WBC-3 and PM1-33 caused decreased PNP degradation rates in both strains and eliminated the difference in PNP degradation between the two strains. Functional prediction using AlphaFold2 showed that protein1619 might bind to p-benzoquinone (BQ). Consequently, protein 1619 was biochemically characterized, confirming its ability to convert BQ into hydroquinone (HQ). Thus, a new protein involved in PNP degradation was identified, thereby adding new knowledge to bacterial PNP degradation pathways.